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AAT Bioquest

XFD405 NHS Ester [equivalent to Alexa Fluor™ 405 NHS Ester]

XFD405, manufactured by AAT Bioquest, is a blue-fluorescent dye that is structurally identical to Alexa Fluor™ 405 (ThermoFisher). This dye is water-soluble and optimized for excitation by the 407 nm krypton laser line or the 408 nm violet laser diode, making it suitable for a range of fluorescence-based techniques. XFD405 is pH-insensitive across a wide range (pH 4 - 10) and exhibits minimal quenching when conjugated to proteins, ensuring consistent fluorescence signals in live-cell imaging. With an excitation maximum at 401 nm and emission at 422 nm, XFD405 is well-suited for multicolor flow cytometry and super-resolution microscopy (STORM), providing reliable performance in applications requiring distinct spectral separation and photostability.

The N-hydroxysuccinimidyl (NHS) ester of XFD405 is a widely used reagent for the conjugation of this dye to proteins or antibodies. NHS esters react selectively and efficiently with primary amines (such as the side chains of lysine residues or aminosilane-coated surfaces) at pH 7-9, forming stable covalent amide bonds. This property makes XFD405 NHS ester an excellent choice for labeling proteins, amine-modified oligonucleotides, and other amine-containing molecules.

Example protocol

PREPARATION OF STOCK SOLUTIONS

Unless otherwise noted, all unused stock solutions should be divided into single-use aliquots and stored at -20 °C after preparation. Avoid repeated freeze-thaw cycles

Protein Stock Solution (Solution A)
  1. Prepare a 1 mL protein labeling stock solution by mixing 100 µL of reaction buffer (such as 1 M sodium carbonate solution or 1 M phosphate buffer, pH ~9.0) with 900 µL of the target protein solution (e.g., an antibody with a protein concentration of at least 2 mg/mL, if possible).

    Note: The pH of the protein solution (Solution A) should be 8.5 ± 0.5. If the pH of the protein solution is lower than 8.0, adjust it to within the 8.0-9.0 range using either 1 M  sodium bicarbonate solution or 1 M phosphate buffer at pH 9.0.

    Note: The protein should be dissolved in 1X phosphate-buffered saline (PBS), pH 7.2-7.4. If the protein is dissolved in Tris or glycine buffer, dialyze it against 1X PBS, pH 7.2-7.4, to remove any free amines or ammonium salts (such as ammonium sulfate and ammonium acetate) commonly used in protein precipitation.

    Note: Antibodies that are impure or stabilized with bovine serum albumin (BSA) or gelatin may not label effectively. Additionally, sodium azide or thimerosal can interfere with the conjugation reaction. To achieve optimal labeling results, these preservatives should be removed through dialysis or spin column techniques.

    Note: For optimal labeling efficiency, it is recommended to maintain a final protein concentration between 2-10 mg/mL. Protein concentrations below 2 mg/mL can significantly reduce conjugation efficiency.

XFD405 NHS Ester Stock Solution (Solution B)
  1. To prepare a 10 mM stock solution of XFD405 NHS ester, add anhydrous DMSO directly to the vial of XFD405 NHS ester. Mix well by pipetting or vortexing.

    Note: Prepare the dye stock solution (Solution B) before starting the conjugation, and use it promptly. Extended storage of the dye stock solution may reduce the dye activity. Solution B can be stored in the freezer for up to two weeks, provided it is protected from light and moisture. Avoid freeze-thaw cycles.

SAMPLE EXPERIMENTAL PROTOCOL

This protocol is designed for labeling Goat anti-mouse IgG with XFD405 NHS ester. Additional optimization may be required to adapt the protocol to your specific proteins.

Note: Each protein requires a distinct dye/protein ratio, which varies depending on the characteristics of the dye. Over-labeling a protein can negatively impact its binding affinity, whereas using a low dye-to-protein ratio in protein conjugates can result in reduced sensitivity.

Run Conjugation Reaction
  1. Use a 10:1 molar ratio of Solution B (dye) to Solution A (protein) as the starting point: Add 5 µL of the dye stock solution (Solution B, assuming the dye stock solution is 10 mM) to the vial containing the protein solution (95 µL of Solution A) with effective shaking. The concentration of the protein is ~0.05 mM, assuming the protein concentration is 10 mg/mL and the molecular weight of the protein is ~200KD.

    Note: We recommend using a 10:1 molar ratio of Solution B (dye)/Solution A (protein). If it is too low or too high, determine the optimal dye/protein ratio at 5:1, 15:1, and 20:1, respectively.

  2. Continue to rotate or shake the reaction mixture at room temperature for 30-60 minutes.

Purify the Conjugate

The following protocol demonstrates the purification of a dye-protein conjugate using a Sephadex G-25 column.

  1. Prepare the Sephadex G-25 column according to the manufacturer's instructions.

  2. Carefully load the reaction mixture (from the "Run Conjugation Reaction" step) to the top of the Sephadex G-25 column.

  3. Add PBS (pH 7.2-7.4) as soon as the sample runs just below the top resin surface.

  4. Add more PBS (pH 7.2-7.4) to the desired sample to complete the column purification. Combine the fractions that contain the desired dye-protein conjugate.

    Note: For immediate use, the dye-protein conjugate must be diluted with staining buffer, and aliquoted for multiple uses.

    Note: For longer-term storage, the dye-protein conjugate solution needs to be concentrated or freeze-dried.

Characterize the Desired Dye-Protein Conjugate

The Degree of Substitution (DOS) is a critical factor in characterizing dye-labeled proteins. Proteins with a lower DOS generally exhibit weaker fluorescence, while those with a higher DOS (e.g., DOS > 6) may also show reduced fluorescence. The optimal DOS for most antibodies typically ranges between 2 and 10, depending on the specific properties of both the dye and the protein. For effective labeling, it is recommended to achieve a DOS of 6-8 moles of XFD405 NHS ester per mole of antibody. The following steps outline the process for determining the DOS of XFD405 NHS ester-labeled proteins.

Measure Absorption

For accurate measurement of the absorption spectrum of a dye-protein conjugate, maintain the sample concentration between 1-10 µM, adjusting as needed based on the dye's extinction coefficient.

Read OD (absorbance) at 280 nm and Dye Maximum Absorption (ƛmax = 401 nm for XFD405 NHS Ester)

For most spectrophotometers, the sample (from the column fractions) needs to be diluted with de-ionized water so that the O.D. values are in the range of 0.1 to 0.9. The O.D. (absorbance) at 280 nm is the maximum absorption of protein, while 401 nm is the maximum absorption of XFD405 NHS ester. To obtain accurate DOS, ensure the conjugate is free of the non-conjugated dye.

Calculate DOS

You can calculate DOS using our tool by following this link:

https://www.aatbio.com/tools/degree-of-labeling-calculator

Spectrum

Product family

NameExcitation (nm)Emission (nm)Extinction coefficient (cm -1 M -1)Quantum yieldCorrection Factor (260 nm)Correction Factor (280 nm)
XFD488 NHS Ester *Same Structure to Alexa Fluor™ 488 NHS Ester*499520710000.9210.300.11
XFD350 NHS Ester *Same Structure to Alexa Fluor™ 350 NHS Ester*34344119000-0.250.19
XFD532 NHS Ester *Same Structure to Alexa Fluor™ 532 NHS Ester*534553810000.6110.240.09
XFD594 NHS Ester *Same Structure to Alexa Fluor™ 594 NHS Ester*590618900000.6610.430.56
XFD555 NHS Ester *Same Structure to Alexa Fluor™ 555 NHS Ester*5535681500000.110.080.08
XFD647 NHS Ester *Same Structure to Alexa Fluor™ 647 NHS Ester*6506712390000.3310.000.03
XFD680 NHS Ester *Same Structure to Alexa Fluor™ 680 NHS Ester*6817041840000.3610.000.05
XFD700 NHS Ester *Same Structure to Alexa Fluor™ 700 NHS Ester*6967191920000.2510.000.07
XFD750 NHS Ester *Same Structure to Alexa Fluor™ 750 NHS Ester*7527762400000.1210.000.04
XFD546 NHS Ester *Same Structure to Alexa Fluor™ 546 NHS Ester*5615721120000.7910.210.12
XFD568 NHS Ester *Same Structure to Alexa Fluor™ 568 NHS Ester*579603913000.6910.450.46
XFD514 NHS Ester *Same Structure to Alexa Fluor™ 514 NHS Ester*51854380000-0.310.18
XFD660 NHS Ester [equivalent to Alexa Fluor® 660 NHS Ester]663691132000-0.000.10
XFD430 NHS ester43254015,000--0.28
QXY21 NHS ester [equivalent to QSY-21 NHS ester]--890001--0.32
Cy5DIGE NHS ester65167025000010.271, 0.420.020.03
Cy2DIGE NHS ester4925081500000.1200.080.15
Cy3DIGE NHS ester55556915000010.1510.070.073
QXY7 NHS ester [equivalent to QSY-7 NHS ester]--900001--0.22
Cy3B NHS ester56057112000010.5810.0480.069
CypHer5E NHS Ester643660----
CypHer7E NHS Ester748769----
Show More (13)

References

View all 6 references: Citation Explorer
Effects of Viscosity and Refractive Index on the Emission and Diffusion Properties of Alexa Fluor 405 Using Fluorescence Correlation and Lifetime Spectroscopies.
Authors: van Zanten, Camila and Melnikau, Dzmitry and Ryder, Alan G
Journal: Journal of fluorescence (2021): 835-845
Egg autofluorescence and options for detecting peanut agglutinin binding for the identification of Haemonchus contortus eggs in fecal samples.
Authors: Abbas, Ibrahim and Hildreth, Michael
Journal: Veterinary parasitology (2019): 69-74
Author Correction: A dynamic three-step mechanism drives the HIV-1 pre-fusion reaction.
Authors: Iliopoulou, Maro and Nolan, Rory and Alvarez, Luis and Watanabe, Yasunori and Coomer, Charles A and Jakobsdottir, G Maria and Bowden, Thomas A and Padilla-Parra, Sergi
Journal: Nature structural & molecular biology (2019): 526
Identification of novel cell-impermeant fluorescent substrates for testing the function and drug interaction of Organic Anion-Transporting Polypeptides, OATP1B1/1B3 and 2B1.
Authors: Patik, Izabel and Székely, Virág and Német, Orsolya and Szepesi, Áron and Kucsma, Nóra and Várady, György and Szakács, Gergely and Bakos, Éva and Özvegy-Laczka, Csilla
Journal: Scientific reports (2018): 2630
Energy transfer between a biological labelling dye and gold nanorods.
Authors: Racknor, Chris and Singh, Mahi R and Zhang, Yinan and Birch, David J S and Chen, Yu
Journal: Methods and applications in fluorescence (2013): 015002
Page updated on October 30, 2024

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Physical properties

Molecular weight

792.64

Solvent

DMSO

Spectral properties

Correction Factor (260 nm)

0.23

Correction Factor (280 nm)

0.70

Extinction coefficient (cm -1 M -1)

35,000

Excitation (nm)

401

Emission (nm)

421

Storage, safety and handling

Certificate of OriginDownload PDF
H-phraseH303, H313, H333
Hazard symbolXN
Intended useResearch Use Only (RUO)
R-phraseR20, R21, R22

Storage

Freeze (< -15 °C); Minimize light exposure
UNSPSC12352200
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